Genetic architecture of cold tolerance in rice (<i>Oryza sativa</i>) determined through high resolution genome-wide analysis

<div><p>Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (<i>Oryza sativa</i> L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 <i>O</i>. <i>sativa</i> accessions representing the five major subpopulations from the <i>INDICA</i> and <i>JAPONICA</i> varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in <i>temperate japonica</i>, six in <i>tropical japonica</i>, 14 in <i>JAPONICA</i>, and nine in <i>INDICA</i>, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the <i>JAPONICA</i> accessions were more tolerant to cold stress than <i>INDICA</i> accessions.</p></div

Gene Ontology (GO) term enrichment analysis of the germination index candidate genes.

<p>The GO analysis describes the gene products in terms of their associated biological processes, cellular components and molecular functions independent of species.</p

Summary statistics for cold tolerance at the germination and reproductive stages.

<p>The mean, range and standard error are given for the germination index (calculated as percent germination in cold divided by warm treatment) based on the two subspecies, <i>INDICA</i> and <i>JAPONICA</i>, and four subpopulations <i>aus</i>, <i>indica</i>, <i>temperate japonica</i> and <i>tropical japonica</i>. At the reproductive stage, 186 <i>JAPONICA</i> accessions which produced panicles were evaluate for three traits.</p

Summary of SNP positions for cold tolerance at the reproductive stage as identified by GWA mapping.

<p>Traits measured were percent sterility, seed weight per panicle and seed weight per plant. All SNPs above the threshold (p-value = 0.0001) are included. Reported QTLs and candidate genes associated with spikelet fertility and seed set which are co-located to these segments are identified.</p

Summary of SNP positions for cold tolerance at germination as identified by GWA mapping.

<p>All SNPs above the threshold (p-value = 0.0001) are included. The accessions were grouped as <i>ALL</i> RDP1 accessions, <i>INDICA</i>, <i>JAPONICA</i>, <i>temperate japonica</i> and <i>tropical japonica</i>. Reported QTLs and candidate genes associated with cold tolerance which are co-located to these segments are identified.</p

plink files for cornell canine dataset

chromosome, name, location, alleles for each SN

plink files for cornell canine dataset

genotypes for each dog at each SN

plink files for cornell canine dataset

ID and sex information for each do

phenotypes

phenotypes for each do